Skill points are earned though collecting secret and general collectables. Make sure you pick up all the collectables you come across and use the maps to make sure you find everyone. Missing a few collectables could cause you to miss out on 1 upgrade.

To earn 15 skill points you will need to finish each stage and get the highest exp score you can. Just collect all the items required below:

You don't need to apply these points to violette but they may help you as you work your way though the game. The more collectables the better, you will need roughly 15,000exp to gain all the points. If you don't want to miss out on this achievement just make sure you pick up all the collectables until you gain the achievement, if you miss something just after a checkpoint load back to the checkpoint and go collect it.

You don't have to get high marks on any level to go towards the EXP, I got the "Soldier" rank on a couple (they pissed me off and I got trigger happy) and still got the achievement. You might want to add that you have to do every "Level Secret" achievement (seven total) for the EXP, on top of all the collectibles.